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Showing content from https://bioconductor.org/packages/devel/bioc/html/../../bioc/html/sangeranalyseR.html below:

Bioconductor - sangeranalyseR (development version)

sangeranalyseR

This is the development version of sangeranalyseR; for the stable release version, see sangeranalyseR.

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

Bioconductor version: Development (3.22)

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

Author: Rob Lanfear <rob.lanfear at gmail.com>, Kuan-Hao Chao <ntueeb05howard at gmail.com>

Maintainer: Kuan-Hao Chao <ntueeb05howard at gmail.com>

Citation (from within R, enter citation("sangeranalyseR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("sangeranalyseR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sangeranalyseR")
Details biocViews Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License GPL-2 Depends R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Imports System Requirements URL See More Suggests testthat (>= 2.1.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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